NM_016023.5(OTUD6B):c.83-2A>G AND Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 3, 2017
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000488135.2

Allele description [Variation Report for NM_016023.5(OTUD6B):c.83-2A>G]

NM_016023.5(OTUD6B):c.83-2A>G

Gene:

OTUD6B:OTU deubiquitinase 6B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q21.3

Genomic location:

Preferred name:

NM_016023.5(OTUD6B):c.83-2A>G

HGVS:

NC_000008.11:g.91071136A>G
NM_001286745.3:c.-361-2A>G
NM_001416022.1:c.83-2A>G
NM_016023.5:c.83-2A>GMANE SELECT
NC_000008.10:g.92083364A>G
NM_016023.3:c.173-2A>G

Nucleotide change:

IVS1AS, A-G, -2

Links:

OMIM: 612021.0003; dbSNP: rs1064797102

NCBI 1000 Genomes Browser:

rs1064797102

Molecular consequence:

NM_001286745.3:c.-361-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001416022.1:c.83-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_016023.5:c.83-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA)
Identifiers:: MONDO: MONDO:0044319; MedGen: C4479520; OMIM: 617452

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000574730	OMIM	no assertion criteria provided	Pathogenic (May 3, 2017)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000574730

OMIM

no assertion criteria provided

Pathogenic
(May 3, 2017)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features.

Santiago-Sim T, Burrage LC, Ebstein F, Tokita MJ, Miller M, Bi W, Braxton AA, Rosenfeld JA, Shahrour M, Lehmann A, Cogné B, Küry S, Besnard T, Isidor B, Bézieau S, Hazart I, Nagakura H, Immken LL, Littlejohn RO, Roeder E; EuroEPINOMICS RES Consortium Autosomal Recessive working group, S. Hande Caglayan., Kara B, et al.

Am J Hum Genet. 2017 Apr 6;100(4):676-688. doi: 10.1016/j.ajhg.2017.03.001. Epub 2017 Mar 23.

PubMed [citation]

PMID:: 28343629
PMCID:: PMC5384096

Details of each submission

From OMIM, SCV000574730.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 sisters, born of consanguineous Palestinian parents (family 5), with intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA; 617452), Santiago-Sim et al. (2017) identified a homozygous A-to-G transition in intron 1 of the OTUD6B gene (c.173-2A-G, NM_016023.3). The mutation was predicted to result in a splice site alteration, the skipping of exon 2, and the introduction of a premature termination codon with nonsense-mediated mRNA decay. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The mutation was not found in the ExAC or gnomAD databases.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 30, 2023

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